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1.
Subst Use Misuse ; 55(1): 108-118, 2020.
Article in English | MEDLINE | ID: mdl-31519121

ABSTRACT

Background: Recovery capital is a theoretical construct elucidating the resources that support recovery from addiction. The 50-item Assessment of Recovery Capital (ARC) instrument and related brief-format versions are the predominant measures of this construct. However, some of the ARC's psychometric properties are not well-established, particularly in racially and economically diverse populations. Objectives: We aimed to determine if the ARC is a valid and reliable measure of recovery capital in a diverse sample. Methods: Paper-and-pencil survey data were collected between March 2017 and May 2018 from a low-income, racially diverse sample of adults in recovery (N = 273). Participants were recruited from nontreatment community settings throughout a mid-sized northeastern U.S. city. They completed the ARC and sociodemographic questions. To determine the ARC's reliability and factor structure, we used item-level analyses and Cronbach's alpha, followed by confirmatory and exploratory factor analyses. Results: Several items performed poorly, having means close to response extremes and problematically small variances. Cronbach's alpha for the full measure was α = .92; however, alphas for the majority of subscales were below .70. The a priori 10-factor model solution failed, preventing interpretation of the confirmatory factor analysis results. Exploratory factor analysis revealed that although the 10-factor model marginally fit the data, items did not load together as proposed. Not once did all five subscale items load highly on the same factor. Conclusions/Importance: The ARC has substantial weaknesses in its theoretical alignment, item performance, and psychometric properties with diverse populations. We recommend the development of a new multidimensional, theory-aligned measure, following a rigorous measurement development protocol.


Subject(s)
Behavior, Addictive/therapy , Poverty/psychology , Substance-Related Disorders/therapy , Adult , Behavior, Addictive/psychology , Factor Analysis, Statistical , Female , Humans , Male , Middle Aged , Psychometrics , Reproducibility of Results , Substance-Related Disorders/psychology
2.
Eur Heart J ; 40(37): 3081-3094, 2019 10 01.
Article in English | MEDLINE | ID: mdl-31114854

ABSTRACT

AIMS: The Brugada syndrome (BrS) is an inherited cardiac disorder predisposing to ventricular arrhythmias. Despite considerable efforts, its genetic basis and cellular mechanisms remain largely unknown. The objective of this study was to identify a new susceptibility gene for BrS through familial investigation. METHODS AND RESULTS: Whole-exome sequencing performed in a three-generation pedigree with five affected members allowed the identification of one rare non-synonymous substitution (p.R211H) in RRAD, the gene encoding the RAD GTPase, carried by all affected members of the family. Three additional rare missense variants were found in 3/186 unrelated index cases. We detected higher levels of RRAD transcripts in subepicardium than in subendocardium in human heart, and in the right ventricle outflow tract compared to the other cardiac compartments in mice. The p.R211H variant was then subjected to electrophysiological and structural investigations in human cardiomyocytes derived from induced pluripotent stem cells (iPSC-CMs). Cardiomyocytes derived from induced pluripotent stem cells from two affected family members exhibited reduced action potential upstroke velocity, prolonged action potentials and increased incidence of early afterdepolarizations, with decreased Na+ peak current amplitude and increased Na+ persistent current amplitude, as well as abnormal distribution of actin and less focal adhesions, compared with intra-familial control iPSC-CMs Insertion of p.R211H-RRAD variant in control iPSCs by genome editing confirmed these results. In addition, iPSC-CMs from affected patients exhibited a decreased L-type Ca2+ current amplitude. CONCLUSION: This study identified a potential new BrS-susceptibility gene, RRAD. Cardiomyocytes derived from induced pluripotent stem cells expressing RRAD variant recapitulated single-cell electrophysiological features of BrS, including altered Na+ current, as well as cytoskeleton disturbances.


Subject(s)
Brugada Syndrome/genetics , Mutation, Missense , Myocytes, Cardiac/pathology , ras Proteins/genetics , Action Potentials/genetics , Adult , Brugada Syndrome/pathology , Brugada Syndrome/physiopathology , Cytoskeleton/genetics , Cytoskeleton/pathology , Female , Genetic Markers , Genetic Predisposition to Disease , Humans , Male , Myocytes, Cardiac/physiology
3.
Comput Human Behav ; 75: 311-319, 2017 Oct.
Article in English | MEDLINE | ID: mdl-34334933

ABSTRACT

Studies of youth social media use (SMU) often focus on its frequency, measuring how much time they spend online. While informative, this perspective is only one way of viewing SMU. Consistent with uses and gratification theory, another is to consider how youth spend their time online (i.e., degree of engagement). We conducted latent profile analyses of survey data from 249 U.S. emerging adults (ages 18-26) to explore their SMU in terms of frequency and engagement. We derived separate 3-profile solutions for both frequency and engagement. High frequency social media users tended to be women and to have more Facebook friends. Highly engaged users (i.e., those most interactive online) tended to be White and more highly educated. Findings from this exploratory study indicate that youth SMU frequency and SMU engagement warrant separate consideration. As SMU becomes more ingrained into the fabric of daily life, it is conceivable that engagement may be a more meaningful way to assess youth SMU, especially in relation to the digital divide, since it can be used to meet important needs, including social interaction, information exchange, and self-expression.

4.
J Am Heart Assoc ; 5(6)2016 06 10.
Article in English | MEDLINE | ID: mdl-27287695

ABSTRACT

BACKGROUND: The Brugada syndrome is an inherited cardiac arrhythmia associated with high risk of sudden death. Although 20% of patients with Brugada syndrome carry mutations in SCN5A, the molecular mechanisms underlying this condition are still largely unknown. METHODS AND RESULTS: We combined whole-exome sequencing and linkage analysis to identify the genetic variant likely causing Brugada syndrome in a pedigree for which SCN5A mutations had been excluded. This approach identified 6 genetic variants cosegregating with the Brugada electrocardiographic pattern within the pedigree. In silico gene prioritization pointed to 1 variant residing in KCNAB2, which encodes the voltage-gated K(+) channel ß2-subunit (Kvß2-R12Q). Kvß2 is widely expressed in the human heart and has been shown to interact with the fast transient outward K(+) channel subunit Kv4.3, increasing its current density. By targeted sequencing of the KCNAB2 gene in 167 unrelated patients with Brugada syndrome, we found 2 additional rare missense variants (L13F and V114I). We then investigated the physiological effects of the 3 KCNAB2 variants by using cellular electrophysiology and biochemistry. Patch-clamp experiments performed in COS-7 cells expressing both Kv4.3 and Kvß2 revealed a significant increase in the current density in presence of the R12Q and L13F Kvß2 mutants. Although biotinylation assays showed no differences in the expression of Kv4.3, the total and submembrane expression of Kvß2-R12Q were significantly increased in comparison with wild-type Kvß2. CONCLUSIONS: Altogether, our results indicate that Kvß2 dysfunction can contribute to the Brugada electrocardiographic pattern.


Subject(s)
Brugada Syndrome/genetics , Gain of Function Mutation/genetics , Potassium Channels, Voltage-Gated/genetics , Electrocardiography , Female , Genetic Predisposition to Disease/genetics , Genotype , Humans , Male , NAV1.5 Voltage-Gated Sodium Channel/genetics , Pedigree , Polymorphism, Single Nucleotide/genetics , Shaker Superfamily of Potassium Channels , Shal Potassium Channels/genetics , Exome Sequencing
5.
Clin J Sport Med ; 26(5): 369-75, 2016 Sep.
Article in English | MEDLINE | ID: mdl-26886802

ABSTRACT

OBJECTIVE: (1) Compare rates of abnormal screening electrocardiograms (ECGs) using updated criteria compared with older criteria. (2) Compare rates of abnormal ECGs by ethnicity. (3) Evaluate ability of ECG criteria to detect the predicted number of athletes with previously undetected cardiovascular abnormalities. DESIGN: Prospective and retrospective review of ECGs. During the prospective portion of the study, the 2005 European Society of Cardiology criteria were used from 2008 to July 2011 and the 2011 Stanford criteria were used from August 2011 to 2013. Retrospectively, all ECGs were reevaluated using the 2011 Stanford criteria, 2013 Seattle criteria, and 2014 Sharma Refined criteria. SETTING: Division I National Collegiate Athletic Association University. PARTICIPANTS: 874 incoming athletes over a 5-year period. INTERVENTIONS: ECG screening program. MAIN OUTCOME MEASURES: Number of abnormal ECGs and number of athletes with newly discovered cardiac abnormalities. RESULTS: Abnormal ECG rates were the 2005 European criteria 10.7%, 2011 Stanford criteria 6.6%, 2013 Seattle criteria 2.8%, and 2014 Sharma Refined criteria 2.8%. In black athletes, the Stanford criteria resulted in more abnormal ECGs compared with Seattle or Sharma Refined. Three athletes were found to have a previously undetected cardiac abnormality (2 with hypertrophic cardiomyopathy and 1 with preexcitation). CONCLUSIONS: More recent ECG screening criteria substantially reduce the abnormal ECG rate and thus the number of athletes requiring additional testing. ECG screening criteria identified the predicted number (1/300) of young athletes with serious underlying cardiovascular disease. These criteria prompt not only additional cardiovascular testing but also a more thorough cardiovascular history.


Subject(s)
Athletes/statistics & numerical data , Cardiovascular Abnormalities/diagnosis , Electrocardiography , Mass Screening , Adolescent , Adult , Cardiovascular Abnormalities/epidemiology , Electrocardiography/standards , Female , Humans , Male , Mass Screening/standards , Prospective Studies , Retrospective Studies , United States/epidemiology , Young Adult
6.
Am J Emerg Med ; 33(3): 423-9, 2015 Mar.
Article in English | MEDLINE | ID: mdl-25618768

ABSTRACT

OBJECTIVES: Most US hospitals lack primary percutaneous coronary intervention (PCI) capabilities to treat patients with ST-elevation myocardial infarction (STEMI) necessitating transfer to PCI-capable centers. Transferred patients rarely meet the 120-minute benchmark for timely reperfusion, and referring emergency departments (EDs) are a major source of preventable delays. We sought to use more granular data at transferring EDs to describe the variability in length of stay at referring EDs. METHODS: We retrospectively analyzed a secondary data set used for quality improvement for patients with STEMI transferred to a single PCI center between 2008 and 2012. We conducted a descriptive analysis of the total time spent at each referring ED (door-in-door-out [DIDO] interval), periods that comprised DIDO (door to electrocardiogram [EKG], EKG-to-PCI activation, and PCI activation to exit), and the relationship of each period with overall time to reperfusion (medical contact-to-balloon [MCTB] interval). RESULTS: We identified 41 EDs that transferred 620 patients between 2008 and 2012. Median MCTB was 135 minutes (interquartile range [IQR] 114,172). Median overall ED DIDO was 74 minutes (IQR 56,103) and was composed of door to EKG, 5 minutes (IQR 2,11); EKG-to-PCI activation, 18 minutes (IQR 7,37); and PCI activation to exit, 44 minutes (IQR 34,56). Door-in door-out accounted for the largest proportion (60%) of overall MCTB and had the largest variability (coefficient of variability, 1.37) of these intervals. CONCLUSIONS: In this cohort of transferring EDs, we found high variability and substantial delays after EKG performance for patients with STEMI. Factors influencing ED decision making and transportation coordination after PCI activation are a potential target for intervention to improve the timeliness of reperfusion in patients with STEMI.


Subject(s)
Emergency Service, Hospital , Myocardial Infarction/therapy , Patient Transfer/statistics & numerical data , Percutaneous Coronary Intervention , Time-to-Treatment/statistics & numerical data , Aged , Cardiac Care Facilities , Electrocardiography , Female , Humans , Male , Middle Aged , Myocardial Infarction/diagnosis , Retrospective Studies , Time Factors
7.
J Am Med Dir Assoc ; 15(9): 671-80, 2014 Sep.
Article in English | MEDLINE | ID: mdl-24721341

ABSTRACT

BACKGROUND: Increasingly, nursing home (NH) providers are adopting a person-centered care (PCC) philosophy; yet, they currently lack methods to measure their progress toward this goal. Few PCC tools meet criteria for ease of use and feasibility in NHs. The purpose of this article is to report on the development of the concept and measurement of preference congruence among NH residents (phase 1), its refinement into a set of quality indicators by Advancing Excellence in America's Nursing Homes (phase 2), and its pilot evaluation in a sample of 12 early adopting NHs prior to national rollout (phase 3). The recommended toolkit for providers to use to measure PCC consists of (1) interview materials for 16 personal care and activity preferences from Minimum Data Set 3.0, plus follow-up questions that ask residents how satisfied they are with fulfillment of important preferences; and (2) an easy to use Excel spreadsheet that calculates graphic displays of quality measures of preference congruence and care conference attendance for an individual, household or NH. Twelve NHs interviewed residents (N = 146) using the toolkit; 10 also completed a follow-up survey and 9 took part in an interview evaluating their experience. RESULTS: NH staff gave strong positive ratings to the toolkit. All would recommend it to other NHs. Staff reported that the toolkit helped them identify opportunities to improve PCC (100%), and found that the Excel tool was comprehensive (100%), easy to use (90%), and provided high quality information (100%). Providers anticipated using the toolkit to strengthen staff training as well as to enhance care planning, programming and quality improvement. CONCLUSIONS: The no-cost PCC toolkit provides a new means to measure the quality of PCC delivery. As of February 2014, over 700 nursing homes have selected the Advancing Excellence in America's Nursing Homes PCC goal as a focus for quality improvement. The toolkit enables providers to incorporate quality improvement by moving beyond anecdote, and advancing more systematically toward honoring resident preferences.


Subject(s)
Nursing Homes/standards , Patient-Centered Care/standards , Quality of Health Care , Aged , Humans , Interviews as Topic , Pilot Projects , Program Development , Quality Indicators, Health Care , Surveys and Questionnaires , United States
8.
PLoS One ; 8(4): e60482, 2013.
Article in English | MEDLINE | ID: mdl-23596509

ABSTRACT

Down syndrome (DS) is caused by trisomy of chromosome 21 (Hsa21) and presents a complex phenotype that arises from abnormal dosage of genes on this chromosome. However, the individual dosage-sensitive genes underlying each phenotype remain largely unknown. To help dissect genotype--phenotype correlations in this complex syndrome, the first fully transchromosomic mouse model, the Tc1 mouse, which carries a copy of human chromosome 21 was produced in 2005. The Tc1 strain is trisomic for the majority of genes that cause phenotypes associated with DS, and this freely available mouse strain has become used widely to study DS, the effects of gene dosage abnormalities, and the effect on the basic biology of cells when a mouse carries a freely segregating human chromosome. Tc1 mice were created by a process that included irradiation microcell-mediated chromosome transfer of Hsa21 into recipient mouse embryonic stem cells. Here, the combination of next generation sequencing, array-CGH and fluorescence in situ hybridization technologies has enabled us to identify unsuspected rearrangements of Hsa21 in this mouse model; revealing one deletion, six duplications and more than 25 de novo structural rearrangements. Our study is not only essential for informing functional studies of the Tc1 mouse but also (1) presents for the first time a detailed sequence analysis of the effects of gamma radiation on an entire human chromosome, which gives some mechanistic insight into the effects of radiation damage on DNA, and (2) overcomes specific technical difficulties of assaying a human chromosome on a mouse background where highly conserved sequences may confound the analysis. Sequence data generated in this study is deposited in the ENA database, Study Accession number: ERP000439.


Subject(s)
Chromosomes, Human , Down Syndrome/genetics , High-Throughput Nucleotide Sequencing , Animals , Chromosomes, Human/radiation effects , Chromosomes, Human, Pair 21 , Comparative Genomic Hybridization , Disease Models, Animal , Gamma Rays/adverse effects , Gene Dosage , Humans , In Situ Hybridization, Fluorescence , Male , Mice , Oligonucleotide Array Sequence Analysis , Recombination, Genetic , Trisomy
9.
Nature ; 496(7446): 498-503, 2013 Apr 25.
Article in English | MEDLINE | ID: mdl-23594743

ABSTRACT

Zebrafish have become a popular organism for the study of vertebrate gene function. The virtually transparent embryos of this species, and the ability to accelerate genetic studies by gene knockdown or overexpression, have led to the widespread use of zebrafish in the detailed investigation of vertebrate gene function and increasingly, the study of human genetic disease. However, for effective modelling of human genetic disease it is important to understand the extent to which zebrafish genes and gene structures are related to orthologous human genes. To examine this, we generated a high-quality sequence assembly of the zebrafish genome, made up of an overlapping set of completely sequenced large-insert clones that were ordered and oriented using a high-resolution high-density meiotic map. Detailed automatic and manual annotation provides evidence of more than 26,000 protein-coding genes, the largest gene set of any vertebrate so far sequenced. Comparison to the human reference genome shows that approximately 70% of human genes have at least one obvious zebrafish orthologue. In addition, the high quality of this genome assembly provides a clearer understanding of key genomic features such as a unique repeat content, a scarcity of pseudogenes, an enrichment of zebrafish-specific genes on chromosome 4 and chromosomal regions that influence sex determination.


Subject(s)
Conserved Sequence/genetics , Genome/genetics , Zebrafish/genetics , Animals , Chromosomes/genetics , Evolution, Molecular , Female , Genes/genetics , Genome, Human/genetics , Genomics , Humans , Male , Meiosis/genetics , Molecular Sequence Annotation , Pseudogenes/genetics , Reference Standards , Sex Determination Processes/genetics , Zebrafish Proteins/genetics
10.
PLoS One ; 7(11): e50233, 2012.
Article in English | MEDLINE | ID: mdl-23209683

ABSTRACT

DNA methylation is one of the most studied epigenetic marks in the human genome, with the result that the desire to map the human methylome has driven the development of several methods to map DNA methylation on a genomic scale. Our study presents the first comparison of two of these techniques - the targeted approach of the Infinium HumanMethylation450 BeadChip® with the immunoprecipitation and sequencing-based method, MeDIP-seq. Both methods were initially validated with respect to bisulfite sequencing as the gold standard and then assessed in terms of coverage, resolution and accuracy. The regions of the methylome that can be assayed by both methods and those that can only be assayed by one method were determined and the discovery of differentially methylated regions (DMRs) by both techniques was examined. Our results show that the Infinium HumanMethylation450 BeadChip® and MeDIP-seq show a good positive correlation (Spearman correlation of 0.68) on a genome-wide scale and can both be used successfully to determine differentially methylated loci in RefSeq genes, CpG islands, shores and shelves. MeDIP-seq however, allows a wider interrogation of methylated regions of the human genome, including thousands of non-RefSeq genes and repetitive elements, all of which may be of importance in disease. In our study MeDIP-seq allowed the detection of 15,709 differentially methylated regions, nearly twice as many as the array-based method (8070), which may result in a more comprehensive study of the methylome.


Subject(s)
Gene Expression Profiling , Gene Expression Regulation , Oligonucleotide Array Sequence Analysis/methods , Sequence Analysis, DNA/methods , CpG Islands , DNA Methylation , Genome, Human , Humans , Immunoprecipitation , Methylation , Reproducibility of Results , Sulfites/pharmacology
11.
Crit Pathw Cardiol ; 11(4): 193-8, 2012 Dec.
Article in English | MEDLINE | ID: mdl-23149361

ABSTRACT

BACKGROUND: The latest American College of Cardiology/American Heart Association guidelines recommend primary percutaneous coronary intervention (PCI) in acute ST-elevation myocardial infarction (STEMI) patients within 90 minutes from presentation to the emergency room. For interhospital transfers, the most recent PCI guidelines recommend first medical contact-to-device times ≤120 minutes. Although PCI-capable hospitals have improved door-to-balloon times, many patients present to non-PCI-capable facilities and have been excluded from national quality measures. METHODS: In our acute myocardial infarction network, not only do we enable non-PCI hospitals to transfer STEMI patients but empower outside emergency medical services (EMS) to activate the catheterization laboratory team with a burst page and transfer STEMI patients directly from the scene. Data on patient characteristics, outcomes, and time elements were collected for "scene STEMI" patients who circumvented outlying rural non-PCI hospitals and are presented in this case series. RESULTS: From December 2007 to November 2010, 22 STEMI patients with higher than average acuity were transported by helicopter directly to our medical center for primary PCI. Median distance from the scene to our medical center was 47 miles [25th to 75th interquartile range (IQR) = 39-71 miles]. Median EMS-to-balloon time was 120 minutes (IQR = 111-134 minutes). There were no false activations by EMS. In comparison, our median time for interhospital STEMI transfers (N = 335) was 145 minutes (IQR = 121-186 minutes) from 2007 to 2009. CONCLUSIONS: In our single-center experience, 22 scene STEMI patients were diagnosed and appropriately triaged by EMS to our center for primary PCI. Our data show feasibility of an EMS-activated STEMI network over long distances with good reperfusion times.


Subject(s)
Air Ambulances , Critical Pathways , Myocardial Infarction/therapy , Patient Transfer/statistics & numerical data , Percutaneous Coronary Intervention , Aged , Biomarkers/analysis , Electrocardiography , Female , Humans , Male , Middle Aged , Risk Factors , Rural Population , Tennessee , Time Factors , Treatment Outcome , Triage
12.
Crit Pathw Cardiol ; 11(3): 91-8, 2012 Sep.
Article in English | MEDLINE | ID: mdl-22825528

ABSTRACT

Out-of-hospital cardiac arrest is common and is associated with high mortality. The majority of in-hospital deaths from resuscitated victims of cardiac arrest are due to neurologic injury. Therapeutic hypothermia (TH) is now recommended for the management of comatose survivors of cardiac arrest. The rapid triage and standardized treatment of cardiac arrest patients can be challenging, and implementation of a TH program requires a multidisciplinary team approach. In 2010, we revised our institution's TH protocol, creating a "CODE ICE" pathway to improve the timely and coordinated care of cardiac arrest patients. As part of CODE ICE, we implemented comprehensive care pathways including measures such as a burst paging system and computerized physician support tools. "STEMI on ICE" integrates TH with our regional ST-elevation myocardial infarction network. Retrospective data were collected on 150 consecutive comatose cardiac arrest victims treated with TH (n = 82 pre-CODE ICE and n = 68 post-CODE ICE) from 2007 to 2011. After implementation of CODE ICE, the mean time to initiation of TH decreased from 306 ± 165 minutes to 196 ± 144 minutes (P < 0.001), and the time to target temperature decreased from 532 ± 214 minutes to 392 ± 215 minutes (P < 0.001). There was no significant change in survival or neurologic outcome at hospital discharge. Through the implementation of CODE ICE, we were able to reduce the time to initiation of TH and time to reach target temperature. Additional studies are needed to determine the effect of CODE ICE and similar pathways on clinical outcomes after cardiac arrest.


Subject(s)
Coma/therapy , Critical Pathways/standards , Emergency Medical Services/methods , Heart Arrest/therapy , Hypothermia, Induced/methods , Aged , Cardiopulmonary Resuscitation , Coma/etiology , Decision Support Systems, Clinical , Female , Heart Arrest/complications , Humans , Male , Middle Aged , Out-of-Hospital Cardiac Arrest/complications , Out-of-Hospital Cardiac Arrest/therapy , Retrospective Studies , Tertiary Care Centers , Treatment Outcome
13.
Nat Genet ; 44(8): 928-33, 2012 Jun 24.
Article in English | MEDLINE | ID: mdl-22729222

ABSTRACT

The phosphatidylinositol 3-kinase (PI3K)-AKT signaling pathway is critical for cellular growth and metabolism. Correspondingly, loss of function of PTEN, a negative regulator of PI3K, or activating mutations in AKT1, AKT2 or AKT3 have been found in distinct disorders featuring overgrowth or hypoglycemia. We performed exome sequencing of DNA from unaffected and affected cells from an individual with an unclassified syndrome of congenital progressive segmental overgrowth of fibrous and adipose tissue and bone and identified the cancer-associated mutation encoding p.His1047Leu in PIK3CA, the gene that encodes the p110α catalytic subunit of PI3K, only in affected cells. Sequencing of PIK3CA in ten additional individuals with overlapping syndromes identified either the p.His1047Leu alteration or a second cancer-associated alteration, p.His1047Arg, in nine cases. Affected dermal fibroblasts showed enhanced basal and epidermal growth factor (EGF)-stimulated phosphatidylinositol 3,4,5-trisphosphate (PIP(3)) generation and concomitant activation of downstream signaling relative to their unaffected counterparts. Our findings characterize a distinct overgrowth syndrome, biochemically demonstrate activation of PI3K signaling and thereby identify a rational therapeutic target.


Subject(s)
Adipose Tissue/enzymology , Adipose Tissue/pathology , Connective Tissue/enzymology , Connective Tissue/pathology , Mutation , Phosphatidylinositol 3-Kinases/genetics , Phosphatidylinositol 3-Kinases/metabolism , Adolescent , Adult , Base Sequence , Bone and Bones/enzymology , Bone and Bones/pathology , Child , Child, Preschool , Class I Phosphatidylinositol 3-Kinases , DNA Mutational Analysis , Enzyme Activation/genetics , Female , Humans , Hyperplasia , Infant , Male , Middle Aged , Mosaicism , Phenotype , Proto-Oncogene Proteins c-akt/genetics , Proto-Oncogene Proteins c-akt/metabolism , Signal Transduction , Syndrome
14.
Eur J Hum Genet ; 19(7): 827-31, 2011 Jul.
Article in English | MEDLINE | ID: mdl-21364695

ABSTRACT

Sequencing the coding regions, the exome, of the human genome is one of the major current strategies to identify low frequency and rare variants associated with human disease traits. So far, the most widely used commercial exome capture reagents have mainly targeted the consensus coding sequence (CCDS) database. We report the design of an extended set of targets for capturing the complete human exome, based on annotation from the GENCODE consortium. The extended set covers an additional 5594 genes and 10.3 Mb compared with the current CCDS-based sets. The additional regions include potential disease genes previously inaccessible to exome resequencing studies, such as 43 genes linked to ion channel activity and 70 genes linked to protein kinase activity. In total, the new GENCODE exome set developed here covers 47.9 Mb and performed well in sequence capture experiments. In the sample set used in this study, we identified over 5000 SNP variants more in the GENCODE exome target (24%) than in the CCDS-based exome sequencing.


Subject(s)
Databases, Genetic , Exons/genetics , Genome, Human/genetics , Open Reading Frames/genetics , Computational Biology , Consensus Sequence/genetics , Genomics , Humans , Polymorphism, Single Nucleotide/genetics , Sequence Analysis, DNA
15.
Article in English | MEDLINE | ID: mdl-22654791

ABSTRACT

Genetic diagnosis of inherited metabolic disease is conventionally achieved through syndrome recognition and targeted gene sequencing, but many patients receive no specific diagnosis. Next-generation sequencing allied to capture of expressed sequences from genomic DNA now offers a powerful new diagnostic approach. Barriers to routine diagnostic use include cost, and the complexity of interpreting results arising from simultaneous identification of large numbers of variants. We applied exome-wide sequencing to an individual, 16-year-old daughter of consanguineous parents with a novel syndrome of short stature, severe insulin resistance, ptosis, and microcephaly. Pulldown of expressed sequences from genomic DNA followed by massively parallel sequencing was undertaken. Single nucleotide variants were called using SAMtools prior to filtering based on sequence quality and existence in control genomes and exomes. Of 485 genetic variants predicted to alter protein sequence and absent from control data, 24 were homozygous in the patient. One mutation - the p.Arg732X mutation in the WRN gene - has previously been reported in Werner's syndrome (WS). On re-evaluation of the patient several early features of WS were detected including loss of fat from the extremities and frontal hair thinning. Lymphoblastoid cells from the proband exhibited a defective decatenation checkpoint, consistent with loss of WRN activity. We have thus diagnosed WS some 15 years earlier than average, permitting aggressive prophylactic therapy and screening for WS complications, illustrating the potential of exome-wide sequencing to achieve early diagnosis and change management of rare autosomal recessive disease, even in individual patients of consanguineous parentage with apparently novel syndromes.

16.
Nat Genet ; 43(1): 23-6, 2011 Jan.
Article in English | MEDLINE | ID: mdl-21131973

ABSTRACT

Functional impairment of DNA damage response pathways leads to increased genomic instability. Here we describe the centrosomal protein CEP152 as a new regulator of genomic integrity and cellular response to DNA damage. Using homozygosity mapping and exome sequencing, we identified CEP152 mutations in Seckel syndrome and showed that impaired CEP152 function leads to accumulation of genomic defects resulting from replicative stress through enhanced activation of ATM signaling and increased H2AX phosphorylation.


Subject(s)
Cell Cycle Proteins/genetics , Genome, Human , Child , Child, Preschool , DNA Damage , Dwarfism/genetics , Facies , Genomic Instability , Histones/genetics , Humans , Male , Microcephaly/genetics , Mutation , Phosphorylation
17.
Nucleic Acids Res ; 39(Database issue): D225-9, 2011 Jan.
Article in English | MEDLINE | ID: mdl-21109532

ABSTRACT

NCBI's Conserved Domain Database (CDD) is a resource for the annotation of protein sequences with the location of conserved domain footprints, and functional sites inferred from these footprints. CDD includes manually curated domain models that make use of protein 3D structure to refine domain models and provide insights into sequence/structure/function relationships. Manually curated models are organized hierarchically if they describe domain families that are clearly related by common descent. As CDD also imports domain family models from a variety of external sources, it is a partially redundant collection. To simplify protein annotation, redundant models and models describing homologous families are clustered into superfamilies. By default, domain footprints are annotated with the corresponding superfamily designation, on top of which specific annotation may indicate high-confidence assignment of family membership. Pre-computed domain annotation is available for proteins in the Entrez/Protein dataset, and a novel interface, Batch CD-Search, allows the computation and download of annotation for large sets of protein queries. CDD can be accessed via http://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml.


Subject(s)
Databases, Protein , Protein Structure, Tertiary , Amino Acid Sequence , Conserved Sequence , Models, Biological , Proteins/classification , Sequence Analysis, Protein
18.
Nat Methods ; 7(2): 111-8, 2010 Feb.
Article in English | MEDLINE | ID: mdl-20111037

ABSTRACT

We have not yet reached a point at which routine sequencing of large numbers of whole eukaryotic genomes is feasible, and so it is often necessary to select genomic regions of interest and to enrich these regions before sequencing. There are several enrichment approaches, each with unique advantages and disadvantages. Here we describe our experiences with the leading target-enrichment technologies, the optimizations that we have performed and typical results that can be obtained using each. We also provide detailed protocols for each technology so that end users can find the best compromise between sensitivity, specificity and uniformity for their particular project.


Subject(s)
Chromosome Mapping/trends , Forecasting , Gene Targeting/trends , In Situ Hybridization/trends , Molecular Probe Techniques/trends , Polymerase Chain Reaction/trends , Sequence Analysis, DNA/trends
19.
Nucleic Acids Res ; 37(Database issue): D205-10, 2009 Jan.
Article in English | MEDLINE | ID: mdl-18984618

ABSTRACT

NCBI's Conserved Domain Database (CDD) is a collection of multiple sequence alignments and derived database search models, which represent protein domains conserved in molecular evolution. The collection can be accessed at http://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml, and is also part of NCBI's Entrez query and retrieval system, cross-linked to numerous other resources. CDD provides annotation of domain footprints and conserved functional sites on protein sequences. Precalculated domain annotation can be retrieved for protein sequences tracked in NCBI's Entrez system, and CDD's collection of models can be queried with novel protein sequences via the CD-Search service at http://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi. Starting with the latest version of CDD, v2.14, information from redundant and homologous domain models is summarized at a superfamily level, and domain annotation on proteins is flagged as either 'specific' (identifying molecular function with high confidence) or as 'non-specific' (identifying superfamily membership only).


Subject(s)
Databases, Protein , Protein Structure, Tertiary , Amino Acid Sequence , Conserved Sequence , Proteins/classification , Sequence Alignment , Sequence Analysis, Protein
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